160 pages ; Glycolytic metabolism of carbohydrates is extensively studied in bacteria, but gluconeogenic carbon sources (e.g., organic acids, aromatic compounds) that feed into the tricarboxylic acid cycle (TCA) are common substrates in environmental matrices and industrial feedstocks. The regulatory mechanisms underlying gluconeogenic carbon catabolism in peripheral pathways and cellular partitioning of fluxes in central carbon metabolism between energy generation and biomass production, however, are not well understood. Metabolic control of cellular fluxes spans from transcriptional or translational regulation to modify enzyme availability to metabolite pools that modulate thermodynamic favorability. In this work, we utilize a multi-omics approach to investigate gluconeogenic metabolic flux networks and corresponding energy and co-factor yields. In chapter 1, we elucidate metabolic bypasses that promote a gluconeogenic fast-growth phenotype in Pseudomonas putida and Comamonas testosteroni, two proteobacterial species with distinct decoupled metabolic networks. In contrast to C. testosteroni, which lacks the enzymes required for both carbohydrate uptake and a complete oxidative pentose phosphate (PP) pathway, P. putida is known to generate surplus NADPH through the oxidative PP pathway. Analysis of the metabolome and proteome demonstrates species-specific regulation of protein abundance but similar reduced carbon investment in phosphorylated metabolites during gluconeogenic feeding on succinate relative to glycolytic feeding on gluconate. Analogous to the genome-based metabolic decoupling in C. testosteroni, our 13C-fluxomics analysis reveals an inactive oxidative PP pathway in P. putida during gluconeogenic feeding, thus requiring transhydrogenase reactions to supply NADPH for anabolism. In chapter 2, we focus on C. testosteroni during growth on aromatic compounds channeled through protocatechuate into central carbon metabolism. We determine transcriptional regulation promotes flux in the peripheral 4,5-meta ...